League of Extraordinary Gentlemen Vols. 1 & 2 did this with Victorian literature. It's very likely that it was this graphic novel that influenced this trope's popularity in the last decade (especially in comics), so it's probably the Trope Codifier. Note that in the movie version a similar Massive Multiplayer Crossover is made mostly for Rule of Funny and Rule of Cool, rather than Deconstruction. Thus, it's not an example of Deconstruction Crossover.

Black Dossier, the sequel to LoEG, did this with mostly 1950s mostly British mostly literature.

League of Extraordinary Gentlemen Vol. 3 is going to do this with, consequently, early 20th century, 1960s and 1990s-2000s fiction.

Albion (created with Alan Moore's assistance) did this with 1950s-'70s British comics published by IPC.

In Twilight of the Superheroes, a script submitted by Alan Moore to DC, he wanted to do the same with the DC Universe.

The original script for Watchmen was this: a crossover of several Charlton Comics characters intended for deconstructing the superhero genre from a modern viewpoint. The final work uses Captain Ersatzes of the Charlton characters instead.

The Anno Dracula series by Kim Newman is a massive hodgepodge of characters vampire and non-vampire, fictional and non-fictional, Victorian and modern, running around in a world where Dracula killed Van Helsing and took over Britain.

Nursery Crime by Jasper Fforde does this with nursery rhyme and fairy tale characters, to the point of postulating an entire murder mystery story around the age-old question of, "Why are the Three Bears' bowls of porridge different temperatures if clearly they were poured at the same time?"

There are some surprisingly convincing Epileptic Trees that interpret Super Smash Bros Brawl as this. One theory states that Master Hand represents the forces of video game order (the rules by which video games function), Crazy Hand represents the forces of video game chaos (the unpredictability that makes video games fun), and Tabuu represents the forces of Serious Business and "Stop Having Fun!" Guys, what with his efforts to imprison Master Hand and destroy the world of video games.

Super Robot Wars Z goes one step further by actually having some characters show in multiple versions of their animated continuities, in order to contrast the differences between them. For example, Classic Ryoma witnesses Armageddon Ryoma and is horrified by his much more violent nature.

It has it's own in universe versions of games like Super Mario Bros., EarthBound, Final Fantasy, and even Deadly Towers and cheesy flash games. It really does well at showing what a character from one genre of games would look like if he was forced into a completely different genre but his character still followed the rules of his original game. For example, how would a platformer character for whom everything does equal damage, and only has four slots in his health bar deal with being put in an RPG where every character has thousands of HP? How would a fighting game character, who needs to take advantage of a character being temporarily stunned after being hit in order to perform combos deal with a platformer character who becomes temporarily invincible after being hit?

Captain SNES fits into this category fairly well. Not only are many of the villains aware that they are merely video game characters (which is, in at least one case, why they became villains to begin with), but characters who travel from one video game world to another are not always prepared for the different rules. (The comic where Magus writes of his experiences learning from Mario seems a good illustration of this.)

The Final Fighting Fantasy Flash series on Newgrounds does a good job at this. For the various Final Fantasy Characters, it starts off as what looks like a simple poorly writen fan fic, but quickly grows the beard and becomes quite epic. It turns out that the legendary weapons of the games where created by the ancients as a way of manipulating the game's protagonists into defeating the forces of evil, and thus restoring balance, however, after evil was defeated, the good guys can't stay around any longer, because they would tip the balance to far towards the light, so, the weapons transport them to another world, where they all meet each other, and (because of the influence the weapons have on their mind) convince them that the characters from the other games are evil, and thus they're forced into a fight to the death. The different characters named "Cid" that appear in every game is actually the same guy, manipulating things from behind the scenes. Unfortunatly, Final Fighting Fantasy has been left unfinished

Marvel DC After Hours does this. Season 1 questions the validity of Superman, Season 2 deals with what the heroes would be like if they all went through what Batman did, and Season 3 revolves around the concept of the Continuity Reboot, and what it would be like to go through one. Of course, by the end, it is always Reconstructed.

Turtles Forever Has the ninja turtles from the 1980 cartoon, the turtles from the 2000s cartoon, and the turtles from the comic meet.

And it. Is. Awesome! Ahem—to clarify how well this actually works as a deconstructive crossover, the antics and personalities of the '80s Turtles—somewhat exaggerated but still grounded in the source material—annoy, confound, and irritate the 2003 turtles to no end. Even Michealangelo, eventually. Then they meet the original turtles (as written in issue 1), and even the 2003 guys seem like plushies by comparison. Yet, in the end, all versions of the Turtles are deemed just as valid as the others.

It's been complained that the 1980 Turtles seem more cowardly. Of course they are; they're in a different world where they are not the main characters, the fourth wall is more rigidly in place, and the Big Bad is both ruthless and competent. Goodbye, Plot Armor.